BioImager.SlideBase Class Reference

Inheritance diagram for BioImager.SlideBase:

Public Member Functions
	SlideBase (BioImage source, SlideImage im, bool enableCache=true)
override IReadOnlyDictionary< string, byte[]>	GetExternImages ()
	Extern image. More...
byte[]	GetTile (TileInfo tileInfo)
Public Member Functions inherited from BioImager.SlideSourceBase
async Task< byte[]>	GetSlice (SliceInfo sliceInfo)
	Get slice. More...
byte[]	GetRgb24Bytes (Image< Rgb24 > image)
abstract IReadOnlyDictionary< string, byte[]>	GetExternImages ()
	Extern image. More...
void	Dispose ()
async Task< byte[]>	GetTileAsync (TileInformation tileInfo)
async Task< byte[]>	GetTileAsync (BruTile.TileInfo tileInfo)
Task< byte[]>	GetSlice (SliceInfo sliceInfo)
	Get slice. More...
IReadOnlyDictionary< string, byte[]>	GetExternImages ()
	Extern image. More...

Static Public Member Functions
static string	DetectVendor (string source)
static byte[]	ConvertRgbaToRgb (byte[] rgbaArray)
Static Public Member Functions inherited from BioImager.SlideSourceBase
static void	Resister (string extensionUpper, Func< string, bool, ISlideSource > factory)
	resister decode for Specific format More...
static ISlideSource	Create (BioImage source, SlideImage im, bool enableCache=true)
static byte[]	ConvertRgbaToRgb (byte[] rgbaArray)

Public Attributes
readonly SlideImage	SlideImage
Public Attributes inherited from BioImager.SlideSourceBase
TileCache	cache = null

Protected Member Functions
void	InitResolutions (IDictionary< int, BruTile.Resolution > resolutions, int tileWidth, int tileHeight)
override void	Dispose (bool disposing)
virtual void	Dispose (bool disposing)

Additional Inherited Members
Static Public Attributes inherited from BioImager.SlideSourceBase
static byte[]	LastSlice
static Extent	destExtent
static Extent	sourceExtent
static double	curUnitsPerPixel = 1
static bool	UseVips = true
Properties inherited from BioImager.SlideSourceBase
static bool	UseRealResolution = true [get, set]
double	MinUnitsPerPixel [get, protected set]
	um/pixel More...
SlideImage	Image [get, set]
ITileSchema	Schema [get, protected set]
string	Name [get, protected set]
Attribution	Attribution [get, protected set]
IReadOnlyDictionary< string, object >	ExternInfo [get, protected set]
	Extern info. More...
string	Source [get, protected set]
	File path. More...
Properties inherited from BioImager.ISliceProvider
double	MinUnitsPerPixel [get]
	um/pixel More...
Properties inherited from BioImager.ISlideExternInfo
string	Source [get]
	File path. More...
IReadOnlyDictionary< string, object >	ExternInfo [get]
	Extern info. More...

Detailed Description

Definition at line 14 of file SlideBase.cs.

Constructor & Destructor Documentation

SlideBase()

BioImager.SlideBase.SlideBase	(	BioImage	source,
		SlideImage	im,
		bool	enableCache = true
	)

Definition at line 17 of file SlideBase.cs.

        {
            Source = source.file;
            SlideImage = im;
            Image = im;
            double minUnitsPerPixel;
            if (source.PhysicalSizeX < source.PhysicalSizeY) minUnitsPerPixel = source.PhysicalSizeX; else minUnitsPerPixel = source.PhysicalSizeY;
            MinUnitsPerPixel = UseRealResolution ? minUnitsPerPixel : 1;
            if (MinUnitsPerPixel <= 0) MinUnitsPerPixel = 1;
            var height = SlideImage.Dimensions.Height;
            var width = SlideImage.Dimensions.Width;
            //ExternInfo = GetInfo();
            Schema = new TileSchema
            {
                YAxis = YAxis.OSM,
                Format = "jpg",
                Extent = new Extent(0, -height, width, 0),
                OriginX = 0,
                OriginY = 0,
            };
            InitResolutions(Schema.Resolutions, 256, 256);
        }

Member Function Documentation

ConvertRgbaToRgb()

static byte[] BioImager.SlideBase.ConvertRgbaToRgb ( byte[]  rgbaArray )

static

Definition at line 97 of file SlideBase.cs.

        {
            // Initialize a new byte array for RGB24 format
            byte[] rgbArray = new byte[(rgbaArray.Length / 4) * 3];
 
            for (int i = 0, j = 0; i < rgbaArray.Length; i += 4, j += 3)
            {
                // Copy the R, G, B values, skip the A value
                rgbArray[j] = rgbaArray[i];     // B
                rgbArray[j + 1] = rgbaArray[i + 1]; // G
                rgbArray[j + 2] = rgbaArray[i + 2]; // R
            }
 
            return rgbArray;
        }

DetectVendor()

static string BioImager.SlideBase.DetectVendor ( string  source )

static

Definition at line 40 of file SlideBase.cs.

        {
            return SlideImage.DetectVendor(source);
        }

Dispose()

override void BioImager.SlideBase.Dispose ( bool  disposing )

protectedvirtual

Reimplemented from BioImager.SlideSourceBase.

Definition at line 132 of file SlideBase.cs.

        {
            if (!disposedValue)
            {
                if (disposing)
                {
                    SlideImage.Dispose();
                }
                disposedValue = true;
            }
            base.Dispose(disposing);
        }

GetExternImages()

override IReadOnlyDictionary< string, byte[]> BioImager.SlideBase.GetExternImages ( )

virtual

Extern image.

Returns

Implements BioImager.SlideSourceBase.

Definition at line 46 of file SlideBase.cs.

        {
            throw new NotImplementedException();
            /*
            Dictionary<string, byte[]> images = new Dictionary<string, byte[]>();
            var r = Math.Max(Schema.Extent.Height, Schema.Extent.Width) / 512;
            images.Add("preview", GetSlice(new SliceInfo { Extent = Schema.Extent, Resolution = r }));
            foreach (var item in SlideImage.GetAssociatedImages())
            {
                var dim = item.Value.Dimensions;
                images.Add(item.Key, ImageUtil.GetJpeg(item.Value.Data, 4, 4 * (int)dim.Width, (int)dim.Width, (int)dim.Height));
            }
            return images;
            */
        }

GetTile()

byte[] BioImager.SlideBase.GetTile

(

TileInfo

tileInfo

)

Definition at line 81 of file SlideBase.cs.

        {
            var r = Schema.Resolutions[tileInfo.Index.Level].UnitsPerPixel;
            var tileWidth = Schema.Resolutions[tileInfo.Index.Level].TileWidth;
            var tileHeight = Schema.Resolutions[tileInfo.Index.Level].TileHeight;
            var curLevelOffsetXPixel = tileInfo.Extent.MinX / MinUnitsPerPixel;
            var curLevelOffsetYPixel = -tileInfo.Extent.MaxY / MinUnitsPerPixel;
            var curTileWidth = (int)(tileInfo.Extent.MaxX > Schema.Extent.Width ? tileWidth - (tileInfo.Extent.MaxX - Schema.Extent.Width) / r : tileWidth);
            var curTileHeight = (int)(-tileInfo.Extent.MinY > Schema.Extent.Height ? tileHeight - (-tileInfo.Extent.MinY - Schema.Extent.Height) / r : tileHeight);
            var bgraData = SlideImage.ReadRegion(tileInfo.Index.Level, (long)curLevelOffsetXPixel, (long)curLevelOffsetYPixel, curTileWidth, curTileHeight);
            //We check to see if the data is valid.
            if (bgraData.Length != curTileWidth * curTileHeight * 4)
                return null;
            byte[] bm = ConvertRgbaToRgb(bgraData);
            return bm;
        }

InitResolutions()

void BioImager.SlideBase.InitResolutions ( IDictionary< int, BruTile.Resolution >  resolutions, int  tileWidth, int  tileHeight  )

protected

Definition at line 113 of file SlideBase.cs.

        {
            for (int i = 0; i < SlideImage.LevelCount; i++)
            {
                /*
                bool useInternalWidth = int.TryParse(ExternInfo.TryGetValue($"openslide.level[{i}].tile-width", out var _w) ? (string)_w : null, out var w) && w >= tileWidth;
                bool useInternalHeight = int.TryParse(ExternInfo.TryGetValue($"openslide.level[{i}].tile-height", out var _h) ? (string)_h : null, out var h) && h >= tileHeight;
 
                bool useInternalSize = useInternalHeight && useInternalWidth;
                var tw = useInternalSize ? w : tileWidth;
                var th = useInternalSize ? h : tileHeight;
                resolutions.Add(i, new Resolution(i, MinUnitsPerPixel * SlideImage.GetLevelDownsample(i), tw, th));
                */
                resolutions.Add(i, new BruTile.Resolution(i, SlideImage.BioImage.GetUnitPerPixel(i), tileWidth, tileHeight));
            }
        }

Member Data Documentation

SlideImage

readonly SlideImage BioImager.SlideBase.SlideImage

Definition at line 16 of file SlideBase.cs.

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The documentation for this class was generated from the following file:

• F:/repos/BioImager/BioImager/Source/Bio/SlideBase.cs